Apparatus for scanning a chemical array

ABSTRACT

A technique for analyzing analytes in a chemical array having a plurality of pixels is provided. The apparatus of the technique contains a light source for irradiating a light beam at the pixels individually, a controller for controlling the relative position of the light source to the array, and a detector for detecting fluorescence resulting from irradiation. The controller controls the light beam generated by the light source to irradiate a first number of pixels sequentially in the array and repeating one or more times the sequential irradiation before irradiating a second number of pixels, the pixels of which are different from those of the first number of pixels. The first number of pixels includes more than one pixel but less than the total number of pixels in the array.

CROSS REFERENCE TO RELATED APPLICATION

This is a divisional of application Ser. No. 08/790,775 filed on Jan.30, 1997, now U.S. Pat. No. 5,837,475 issued on Nov. 17, 1998.

FIELD OF THE INVENTION

The present invention relates to detecting chemicals in a chemical arrayand, more particularly, to improving the signal to noise ratio byrepeating scanning of the pixels of the array.

BACKGROUND

Recently, chemical arrays, more particularly, biomolecular arrays, havebeen successfully created. For example, Fodor, et al., "Light-directed,Spatially Addressable Parallel Chemical Synthesis," Science, Vol. 251,767-773 (1991) disclose high density arrays formed by light-directedsynthesis. The array was used for antibody recognition. Biomoleculararrays are also described by E. Southern (PCT Publication WO 89/10977)for analyzing polynucleotide sequences. Such biomolecular arrays lendthemselves to a large number of applications, from DNA and proteinsequencing to DNA fingerprinting and disease diagnosis.

A typical approach for synthesizing a polymer array on an opticalsubstrate is described by Fodor et al. (1991) supra; PCT publications WO91/07087, WO 92/10587, and WO 92/10588; and US Pat. No. 5,143,854. Insuch arrays, different receptors are synthesized onto a substrate usingphotolithographic techniques. Ligands are washed over the array. Eitherthe ligand is fluorescently labeled or an additional fluorescentlylabeled receptor is also washed over the array. The result is thatfluorophores are immobilized on those pixels where binding has occurredbetween the ligand and the receptor(s). In general, a chemical array isilluminated with radiation that excites the fluorophores. The pattern ofbright and dark pixels is recorded. Information about the ligand isobtained by comparing this bright-dark pattern with known patterns ofsurface bound receptors.

In many application, e.g., in analyzing the human genome, it is oftennecessary to scan a large number of array elements. Therefore, theability to read a chemical array with a large number of elements withina short time is highly desirable. Lasers have been used to impinge onchemical array elements with a small spot size beam of high intensity.

SUMMARY

The present invention provides an apparatus and technique for analyzingchemicals in a chemical array that is scanned, i.e., read by irradiatingand detecting any resulting light interaction such as fluorescence, inlines of pixels. Some of the pixels are suspected to contain targetchemicals that contain a fluorescent material. The apparatus includes alight source, a controller, and a detector. The light source is used forirradiating a light beam at the pixels individually. The light sourcemay contain a light generator, such as a laser, and a mechanism fordirecting a light beam from the light generator, such as a scanner. Thecontroller controls the relative position of the light source to that ofthe pixels such that the light source directs the light beam toirradiate pixels in a set sequentially in the array. The sequentialirradiation is repeated on the set of pixels one or more times before asecond set of pixels, which contains pixels different from those in thefirst set of pixels, are irradiated. The first set of pixels has morethan one pixel but less than the total number of pixels in the array.The detector is used for detecting fluorescence resulting from theirradiation on the array.

The apparatus and technique of the present invention can beadvantageously used to analyze chemical arrays, particularly largechemical arrays that contain thousands or millions of small pixels, whenscanned. By allowing adequate time for the dye molecules in the pixelsto recover from metastable states, which can not fluoresce, more signalscan be obtained to improve the signal-to-noise ratio without increasingthe excitation beam intensity. However, by reducing the time beforerepeating the irradiation of the a pixel and the distance traversed bythe beam between re-irradiations (i.e., repeating irradiation) of apixel, more accurate superposition is achieved, leading to more reliabledata.

BRIEF DESCRIPTION OF THE DRAWINGS

The following figures show the embodiments of the present invention tobetter illustrate the apparatus and technique of the present invention.In these figures, like numerals represent like features in the severalviews and the drawings are not drawn to scale for the sake of clarity.

FIG. 1 shows a schematic representation of an apparatus according to thepresent invention.

FIG. 2 shows a schematic representation of further details of anapparatus according to the present invention.

FIG. 3 is a flow diagram showing the process of reading a chemical arrayaccording to the present invention.

FIG. 4 shows a schematic representation to illustrate some of the energylevels of a dye.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides an improved technique for analyzingchemical array by repeating illumination and detecting the resultingfluorescence of a set of pixels in the array before moving to anotherset of pixels. In each set of pixels, all the pixels are illuminatedsequentially before repeating. This improves the signal to noise ratioby allowing adequate time for the dye to recover from metastable statesbefore it is illuminated again.

As used herein, an "array" is an arrangement of objects in space inwhich each object occupies a separate predetermined spatial position.Each of the objects or array elements (which may contain many pixelswhen scanned with light pulses) in the array in an apparatus of thisinvention contains one or more species of binder chemical moieties forbinding specific analytes, such that the physical location of eachspecies of analytes is known or ascertainable. "Pixel" are spots of anarray, which spots are illuminated and the resultant light from thespots is detected as discrete elements to form an image pattern when thearray is being analyzed. An "analyte" is a molecule whose detection in asample is desired and which selectively or specifically binds to abinder chemical moiety, such as a molecular probe. An analyte can be thesame or a different type of molecule as the molecular probe to which itbinds.

FIG. 1 shows a schematic representation of an apparatus for analyzingchemical arrays according to the present invention. The apparatus 100contains a light source (e.g., laser) 102 for emitting a light of awavelength and with sufficient intensity to cause fluorescence in aselected fluorescent material. Often, the excitation light intensity issufficiently high such that the dye used in the chemical array 104approaches metastable state saturation, i.e., some of the dye moleculescross into metastable states. A controller 108 directs the light fromthe light source 102 to impinge on the elements of the array one pixelat a time. This can be accomplished, for example, by using a controllerto change the relative position of the light source 102 to the chemicalarray 104, e.g., by moving the light generator (e.g., a laser) in thelight source, moving the chemical array, or steering a light beam, e.g.,by using a scanner, such that different pixels can be illuminated atdifferent time. Typically, the light beam is directed by translation ofthe array on an object table 217 (not shown in FIG. 1 but shown in FIG.2) or scanning the light beam with a beam scanner. The dye, when excitedby the excitation light from the light source 102, emits fluorescence,which is detected by a detector 110. The fluorescence intensity can alsobe measured.

FIG. 2 shows in further detail an embodiment of the apparatus of FIG. 1.The apparatus 200 has a laser 204, which emits an excitation laser beam.A scanner 208 directs the laser beam through an optics system 212 to achemical array 216 to cause fluorescence. The optics system 212 cancontain, for example, collimating optics such as lenses and prisms tofocus the laser light on the pixels in the chemical array.

Fluorescent light resulting from the array being irradiated by the laserlight is collected by an optics system 220, which can contain, forexample, lenses and prisms to direct the fluorescent light to a detector224. The optics systems 220 can also contain filters and apertures tofilter out unwanted light such as excitation light. A controller 228 iselectrically connected to the detector 224 for collecting electricalsignals generated in the detector as a result of fluorescent lightimpinging on the detector. The controller 228 is connected to thescanner 208 such that each fluorescent light signal received by thedetector 224 can be traced to the pixel from which the fluorescent lightsignal is generated. The controller 228 is further connected to thelaser 204 and may be used to control the laser to emit light pulses of aspecific duration. The scanner 208 is used to move the laser beam from apixel to another between pulses. However, if desired, the laser can emita continuous beam as the scanner directs the laser beam from pixel topixel. Alternatively, instead of scanning, i.e., moving, the excitationbeam, the chemical array 216 can be controlled to translate to positiondifferent pixels under the focused excitation beam at different times.Another alternative is to control to physically move the laser 204 todirect the laser beam at different pixels.

The data of signals received by the controller 228 can be processed todetermine the presence or quantity of analytes in the pixels. To achievethis, the controller 228 can contain a microprocessor or a computer toprocess the information on pixel locations and fluorescence. The signalsfrom the detector 224 or the information from the controller 228 canfurther be transmitted to another processor 232 for further dataprocessing and to a storage device 236, such as disk, tapes, compactdisk, and the like. The information from the controller 228 or processor232 can also be displayed in a display device 240 such as a cathode raytube, plotter, printer, and the like. If desired, different computersand microprocessors can be used to control the light beam/pixel relativeposition and for linking the data of pixel position and fluorescencepattern.

METHOD OF READING ARRAY

FIG. 3 shows the technique for analyzing, i.e., reading, or scanning(i.e., read) pixels in a chemical array according to the presentinvention. Typically the array includes array elements, which when readby irradiation and detection of fluorescence, result in pixels that arearranged in rows and columns, each of which may be considered a line.For illustration, we call a row a line. A set of pixels are selectedfrom the array (step 304). The first pixel in the set is irradiated witha laser beam for a specific duration, e.g. a few microseconds and theresultant fluorescence is detected or measured (step 306). The otherpixels in the set are similarly treated, i.e., irradiated and theresultant fluorescence (step 310) detected sequentially one pixel at atime. After the last pixel in the set has been read once by irradiationand detection the pixels are read again one or more times (steps 314 and318) in a manner similar to the first reading. Other sets of pixels inthe array are selected and read as done with the first set until all thepixels have been read (step 322). Generally, this means all the arrayelements have been read.

Preferably, each of the sets includes pixels that are physically closetogether so that the movement of the actuating mechanism, e.g., scanner,for moving the relative location of light beam to pixels, is notextensive when moving from pixel to pixel in irradiation andre-irradiation. For example, the set can be a number of pixels (i.e., asubset of pixels) in a line. More preferably, the set is a line (e.g., arow or a column) to facilitate the smooth movement of scanning mechanismto scan sequentially the pixels in the set. If desired, the set caninclude a portion of a line or more than one line. As previously stated,the number of pixels in a set is selected such that adequate time isallowed for the recovery of the pixels from the metastable states.

SELECTING TIME BEFORE REPEATING IRRADIATING A PIXEL

In a laser induced fluorescence scanner with small spot size (e.g.,about 3 μm FWHM Gaussian beam), the laser light excites the fluorophore(i.e., dye) molecules and cause fluorescence. The fluorescence isdetected to indicate the presence of the fluorophore molecules, andtherefore the presence of analytes that are attached to fluorophoremolecules. FIG. 4 is a schematic representation showing the energy leveltransition when a dye is excited. When a dye molecule absorbs laserlight (arrow E), it is excited from the ground state energy level G, tothe energy level H. From energy level H the dye molecule falls back tothe ground state (arrow F), releasing light as fluorescence.

To produce better signals, fairly high intensity laser is used, since toa degree higher intensity excitation light (i.e., light from the laser)produces more fluorescence photons. Because of the intensity of thelaser light impinging on the dye, the dye molecules may, depending onthe nature of the particular dye, cross (e.g., from the exited energylevel H) into metastable state(s) (or long-life-quasi-stable-state(s)),such as the triplet state. As used herein, the term "metastable state,"or "long-life-quasi-stable-state" of a dye molecule refers to an energystate in which the dye molecule has higher than the ground state energylevel but loses its energy, converting to the dye ground state, an orderof magnitude or more slower than the singlet state fluorescence.Depending on the particular dye, many different metastable states arepossible. An important example of a metastable state is the tripletstate. Other metastable states include the biradical state, and theion-pair state. Although many metastable states may be possible, for thesake of clarity, in FIG. 4, the metastable states are shown as M, towhich transition from energy level H is represented by arrow L. At theirmetastable states, the dye molecules convert back to the ground statemuch more slowly than in the singlet state fluorescence, which is shownby arrow F. From the metastable states, the fluorescent material (i.e.,dye molecules) does not release light of a wavelength same as that ofthe fluorescence of arrow F. Therefore, any dye molecule that crosses tothe metastable state is lost to fluorescence. Since a dye molecule at ametastable state cannot fluoresce, this phenomenon appears as saturationof the fluorescence signal. In this situation, increasing laser power,i.e., the intensity of illumination on an array element, will notincrease the number of detected fluorescence photons proportionally.

For systems limited by photon shot noise in their performance, whensaturation is occurring, the signal-to-noise ratio can only be increasedmarginally, if at all, by scanning more slowly or with higherillumination power. In the present invention, we scan a set (or anumber) of pixels in the chemical array two ore more times to increasethe signal-to-noise ratio. Furthermore, we wait for a period of time forthe molecules in the dye in a pixel to recover sufficiently, preferablysubstantially, from their metastable states before re-irradiating thepixel. To this end, a set, i.e., a number, of pixels are irradiatedsequentially, each for short duration (e.g., a few microseconds) suchthat by the time the last pixel in the set is irradiated, the firstpixel has recovered from the metastable state.

The time period (herein referred to as the "rest period") to be selectedfor the dye in a pixel to recover from the metastable states beforere-irradiating depends on the nature of the dye. Many commonly used dyeshave recovery time constants of metastable states in the range of about10⁻⁵ S to 10⁻¹ S. For this reason, a rest period of about 10⁻⁵ S to 10⁻¹S would be adequate for the dye in a pixel to substantially recover fromits metastable states. In contrast, the fluorescence time constant is inthe range of nanoseconds. Generally, the rest period of a few of thecommonly used dyes are known in the art. The rest period of a dye canalso be determined by a method as described below. The number of pixelsto be included in a set depends on the illumination time for a pixel andthe recovery time (or rest period) of the dye. Generally, 100 or more ofpixels, preferably more than about 1000 pixels, are included in a set ofpixels to be read sequentially before re-irradiation.

To determine the rest period of a dye, the following technique can beused. The dye of interest is subjected to light from an irradiationsource, which is turned on rapidly relative to the dye rest period whilethe temporal evolution (i.e., the time dependence of the fluorescentintensity) of the fluorescent intensity is monitored. The fluorescentintensity is the highest initially but it decreases to a lower levelover time. The time to reach the lower intensity level is closelyrelated to the dye rest period. Decrease in the fluorescent intensityreflects the level of saturation. Data obtained can be fitted to amathematical model to obtain time constants of the change in intensity.Methods of modeling to obtain time constants are known in the art.Generally, the dye is considered to have sufficiently recovered from themetastable states after about one time constant. It is considered tohave substantially recovered from the metastable states after about 2time constants.

Examples of suitable dyes (i.e., fluorescent material) that can be usedas labels for the present invention include dyes well known to oneskilled in the art, such as fluoresceins, TEXAS RED, ethidium bromide,chelated lanthanides, rhodamines, indocyanines, carbocyanines, oxazines,organometallics, and metal atom cluster compounds. The rest period,i.e., time needed for recovery from the metastable states of these dyes,can be determined with the technique described in the above.

A variety of suitable light-emitting devices can be used as the lightgenerator in the light source. Such light-emitting devices are known inthe art. They include, for example, light emitting diode (LED) andlasers, such as diode lasers, gas lasers, e.g., HE-NE laser, Ar ionlaser, frequency doubled Neodynium-glass laser, nedium YAG laser, fiberlaser, or other solid-state lasers. The pixels in the array can bearranged in a flat pattern. An alternative is arranging the pixels in acircular pattern as on a cylindrical surface. Generally, the pixels areheld in a pattern of rows and columns. Since we know the origin of eachpixel, we know the binder chemical moieties in the pixel. Iffluorescence is detected for the pixel, we will know the identity of theanalyte bound to that pixel.

ARRAY LIGHT DETECTION

A detector is used for detecting the light resulting from fluorescencein the array. For example, a single element optical detector, e.g., aPNT photomultiplier tube, may be used. Since the time of a light beambeing directed at any particular pixel is known and the illumination ofdifferent pixels are temporally spaced apart, the correspondingfluorescence detected will indicate the presence of fluorescent materialin the pixel. An alternative detector is an array detector in which morethan one detector element is used to over-sample the target chemicals,permitting the discrimination against non-uniformities. One example ofan array detector is a solid-state semi-conductor device, such as acharge-coupled device (CCD) array.

The excitation light from a light source impinges on the fluorescentmaterial bound to the analyte in the array and causes it to emit lightas fluorescent light. Only pixels with a fluorescent material will emitfluorescence signal. The detected fluorescent signals are identifiedwith electronic excitation for light sources and processed, preferablyby an electronic processing unit, such as a microprocessor or acomputer.

As previously stated, by analyzing the pattern of the fluorescence lightin the array, the identity of the analytes in the sample can bedetermined. Detecting fluorescence with a suitable detector will resultin the pattern of fluorescence, in which certain locations in thepattern show fluorescence and certain locations do not. The identity ofan analyte on a particular pixel in the array can be determined bydetecting the location of the fluorescence in the pattern and linkingthis location with data concerning the identity of binder chemicalmoieties and pixel positions in the array. There are various methods forlinking such data with the chemical array. For example, the data can bephysically encoded on the array's housing or stored separately in acomputer.

The present technique of irradiation and detection has a great advantageover techniques that require re-irradiation after reading each pixel orre-irradiate only after the whole array has been read. If there-irradiation of a pixel is done immediately after the pixel has beenirradiated, the dye molecules in the pixel may not have enough time torecover sufficiently from the metastable states and fluorescence is lessthan optimal due to the presence of metastable states, which do notfluoresce. However, if re-irradiation is done only after the whole arrayor a large section, such as half, of the array has been irradiated, theactuating or beam steering mechanism would have to move a substantialdistance and wait a long time before going back to the first array. Thisis particularly true for large arrays (e.g., those having more than athousand, or even having thousands of pixels in a row or column) withsmall and closely adjacent pixel dimensions of today. For example, thedimension of a pixel can be as small as 3 μm across. In traversing asubstantial distance and waiting a long time, the original pixelspositions may not be reestablished (i.e., superpositioned) easily. Forexample, the temperature may have changed, thereby causing the array tochange in size. For example, thermal expansion can occur if the arrayhas been stored in below room temperature before reading in roomtemperature. In the present invention, adequate time is taken for thedye in a pixel to recover from the metastable states, but not so muchtime that it increases substantially the difficulty in superpositioningthe laser beam at the original locations. The result of rescans (i.e.,re-readings) can be added or averaged on line to reduce the amount ofdata to be stored.

As previously stated, the control of the actuating or beam-steeringmechanism, e.g., the scanner for moving the laser beam, the actuatingsystem for moving the array, or the actuator that moves the laser, canbe done by a computer. Generally, a computer program, or software can beimplemented to accomplish such control, as well as the detection andmeasurement of the fluorescence. The control of actuators, scanners,etc., are well known in art.

In the analysis of data, the fluorescence intensity of each reading of apixel is stored in the memory of a computer (which can also be amicroprocessor). After each re-irradiation and re-detection, the memoryis updated by summing the old and new fluorescence data for each pixel.In the absence of bleaching of the dye, the signals increaseproportionally to the number n of the repeated readings and thesignal-to-noise ratio scales as the square root of n.

For illustration purposes, the following example is given. However, oneskilled in the art will be able to adapt the disclosed example for otherapplications. A UNIPHASE (San Jose, Calif.), model 2211-20SLE laseroperating at an output power of 10 mW, wavelength of 488 nm, and a focalspot of 3 μm full-width-half-maximum (FWHM) was used to scan a chemicalarray having 5000 pixels in a row. The irradiation duration was at least5 μs for each pixel, for example, 6 μs. A fluorescein, which has afluorescence lifetime in the order of nanoseconds, was the dye forlabeling the analytes. The time needed for recovery from the metastablestates of the fluorescein was in the order of milliseconds. By scanningone line, i.e., 5000 pixels, before re-irradiation, the line time, i.e.,time needed to finish a line before repeating, is at least about 30 ms,which is ample for the fluorescein to recover from its metastablestates.

Although the illustrative embodiments of the apparatus of the presentinvention and the methods of making and using the apparatus have beendescribed in detail, it is to be understood that the above-describedembodiments can be modified by one skilled in the art, especially insizes and shapes and combination of various described features withoutdeparting from the scope of the invention. Although the theory outlinedin the present disclosure is believed to be accurate, the application ofthe present invention is not dependent on any theory described herein.

What is claimed is:
 1. An apparatus for analyzing chemicals in an arrayhaving a plurality of array elements some of which are suspected tocontain fluorescent material, comprising:(a) a light source forirradiating a light beam at the elements in individual pixels, thepixels being arranged in lines; (b) computer means for controlling therelative position of the light source to the array such that the lightsource directs the light beam to irradiate a first number of pixelssequentially in the array and repeating one or more times the sequentialirradiation before irradiating a second number of pixels, the pixels ofwhich are different from the first number of pixels, the first number ofpixels having more than one pixel and less than the total number ofpixels in the array such that a period elapses adequate for thefluorescent material in a pixel to recover from a metastable statebefore the pixel is irradiated again; and (c) detector for detectingfluorescence resulting from the irradiation.
 2. The apparatus accordingto claim 1 wherein the means for controlling is adapted to direct lightat the first number of pixels being irradiated before repeating suchthat a period elapses adequate for the fluorescent material in a pixelto substantially recover from its triplet excited state before the pixelis irradiated again.
 3. The apparatus according to claim 1 wherein atleast a portion of the light source is movable and the means forcontrolling is adapted to move the at least a portion of the lightsource to direct the light beam from pixel to pixel to irradiate thepixels.
 4. The apparatus according to claim 1 wherein the controllingmeans is adapted to control the light source to irradiate the pixels ina line sequentially and repeat one line at a time from adjacent line toadjacent line, without irradiating a line after another line has beenirradiated thereafter.
 5. The apparatus according to claim 1 furthercomprising a means to sum fluorescence signals detected from a pixel bythe detector during repeated irradiation of the pixel.
 6. The apparatusaccording to claim 1 wherein the light source is adapted to emit a lightsuitable for causing fluorescence in a fluorescent material selectedfrom the groups consisting of fluoresceins, TEXAS RED, ethidium bromide,chelated lanthanides, rhodamines, indocyanines, carbocyanines, oxazines,organometallics, and metal atom cluster compounds.
 7. The apparatusaccording to claim 1 further comprising an object table on which thearray can be placed for the translation of array wherein the means forcontrolling is adapted to control the object table to move the array toposition the pixels to be irradiated from pixel to pixel.
 8. Theapparatus according to claim 1 further comprising an object table onwhich an array having lines of pixels which have 100 or more pixels perline can be placed, wherein the means for controlling is adapted tocontrol the relative movement of the array to the light source toirradiate from pixel to pixel.
 9. The apparatus according to claim 1further comprising an object table for holding an array having aplurality of lines of pixels, each line have 100 or more pixels, whereinthe means for controlling is adapted to control movement of the array toirradiate from pixel to pixel.
 10. An apparatus for analyzing chemicalsin an array having a plurality of array elements some of which aresuspected to contain fluorescent material, the apparatus comprising:(A)light source for irradiating a light beam at the elements in individualpixels, the pixels being arranged in lines; (B) detector for detectingfluorescence resulting from the irradiation; (C) processor forcontrolling the relative position of the light source; (D) programstorage medium that tangibly embodying a program code means readable bythe processor for causing the processor to analyze the chemical array,the program code means including:(i) code means for controlling therelative position of the light source to the array to irradiate a firstnumber of pixels sequentially in the array elements and to detect thefluorescence resulting from the irradiation in the pixels, the firstnumber of pixels being more than one pixel and less than the totalnumber of pixels in the array and such that a period elapses adequatefor the fluorescent material in a pixel to recover from a metastablestate before the pixel is irradiated again; and (ii) code means forcontrolling the relative position of the light source to the array torepeat the irradiation and detecting on the first number of pixels oneor more times before irradiating pixels of a second number of pixelsthat are different from the pixels of the first number of pixels in thearray.
 11. The apparatus according to claim 10 further comprising codemeans for selecting the first number of pixels based on information onthe adequate period for the fluorescent material in a pixel to recoverfrom a metastable state.
 12. The apparatus according to claim 10 whereinthe code means for controlling the irradiation of the first number ofpixels controls the irradiation before repeating such that a periodelapses adequate for the fluorescent material in a pixel tosubstantially recover from its triplet excited state before the pixel isirradiated again.
 13. The apparatus according to claim 10 wherein thecode means for controlling to repeat the irradiation controls to move anirradiating light beam from pixel to pixel in a line of pixels andrepeating the irradiating of the same line at least once before movingon to another line of pixels.
 14. The apparatus according to claim 10wherein the first number of pixels is the number of pixels in a firstline and the second number of pixels is the number of pixels in a lineadjacent to the first line in the array, each line having more than 100pixels.
 15. The apparatus according to claim 10 wherein the code meansfor controlling to repeat the irradiation controls to irradiate pixelsin a line sequentially and to repeat before irradiating another line,substantially all of the lines are irradiated one line at a time fromone adjacent line to the next, for all the lines of pixels withoutre-irradiating a line once a different line has been irradiatedthereafter.
 16. The apparatus according to claim 10 wherein the codemeans controls to irradiate an adequate of number pixels in a line suchthat 10⁻⁵ second to 10⁻¹ second has elapsed before a pixel isre-irradiated.
 17. The apparatus according to claim 10 wherein the lightsource is adapted to emit a light suitable for causing fluorescence in afluorescent material selected from the groups consisting offluoresceins, TEXAS RED, ethidium bromide, chelated lanthanides,rhodamines, indocyanines, carbocyanines, oxazines, organometallics, andmetal atom cluster compounds and wherein the code means furthercomprising code means for selecting the first number of pixels based oninformation on the adequate period for the selected fluorescent materialin a pixel to recover from a metastable state.
 18. An apparatus foranalyzing chemicals in an array having a plurality of array elementssome of which are suspected to contain fluorescent material, theapparatus comprising:(A) light source for irradiating a light beam atthe elements in individual pixels, the pixels being arranged in lines;(B) detector for detecting fluorescence resulting from the irradiation;(C) processor for controlling the relative position of the light source;(D) program storage medium tangibly embodying a program code meansreadable by the processor for causing the processor to analyze thechemical array, the program code means including:(i) code means forcontrolling the relative position of the light source to the array toirradiate a line of pixels sequentially in the array elements and todetect the fluorescence resulting from the irradiation in the pixels,the line of pixels having more than 100 pixels and less than the totalnumber of pixels in the array, the number of pixels in a line beingsufficiently large such that a period would elapse adequate for thefluorescent material in the pixel first irradiated to recover from ametastable state before the whole line has been irradiated; (ii) codemeans for controlling the relative position of the light source to thearray to repeat the irradiation and detect on the first line of pixelsone or more times before irradiating pixels of a second line of pixels,such that 10⁻⁵ second to 10⁻¹ second has elapsed before a pixel isre-irradiated, and to irradiate and detect in like manner all of thearray elements until all the array elements have been irradiated withoutre-irradiating any line of pixels after another line has been irradiatedsubsequent to the irradiation of that any line.
 19. An article ofmanufacture comprising a program storage medium, tangibly embodying aprogram code means readable by a computer for causing the computer tocontrol the analysis of a chemical array by irradiation resulting influorescence, the program code means including:(i) code means forcontrolling the relative position of a light source to the array toirradiate a first number of pixels sequentially in array elements of thearray and to detect the fluorescence resulting from the irradiation inthe pixels, the first number of pixels being more than one pixel andless than the total number of pixels in the array and such that a periodelapses adequate for the fluorescent material in a pixel to recover froma metastable state before the pixel is irradiated again; and (ii) codemeans for controlling the relative position of the light source to thearray to repeat the irradiation and detecting on the first number ofpixels one or more times before irradiating pixels of a second number ofpixels that are different from the pixels of the first number of pixelsin the array.
 20. An apparatus for analyzing chemicals in an arrayhaving a plurality of array elements some of which are suspected tocontain fluorescent material, comprising:(A) a light source forirradiating a light beam at the elements in individual pixels, thepixels being arranged in lines; (B) means for controlling the relativeposition of the light source to the array such that the light sourcedirects the light beam to irradiate a first number of pixelssequentially in the array and repeating one or more times the sequentialirradiation before irradiating a second number of pixels, the pixels ofwhich are different from the first number of pixels, the first number ofpixels having more than one pixel and less than the total number ofpixels in the array such that a period elapses adequate for thefluorescent material in a pixel to recover from a metastable statebefore the pixel is irradiated again; and (C) detector for detectingfluorescence resulting from the irradiation; wherein at least a portionof the light source is movable and the means for controlling is adaptedto move the at least a portion of the light source to direct the lightbeam from pixel to pixel to irradiate the pixels.
 21. An apparatus foranalyzing chemicals in an array having a plurality of array elementssome of which are suspected to contain fluorescent material, theapparatus comprising:(A) light source for irradiating a light beam atthe elements in individual pixels, the pixels being arranged in lines;(B) detector for detecting fluorescence resulting from the irradiation;(C) processor for controlling the relative position of the light source;(D) program storage medium that tangibly embodying a program code meansreadable by the processor for causing the processor to analyze thechemical array, the program code means including:(i) code means forcontrolling the relative position of the light source to the array toirradiate a first number of pixels sequentially in the array elementsand to detect the fluorescence resulting from the irradiation in thepixels, the first number of pixels being more than one pixel and lessthan the total number of pixels in the array and such that a periodelapses adequate for the fluorescent material in a pixel to recover froma metastable state before the pixel is irradiated again; (ii) code meansfor controlling the relative position of the light source to the arrayto repeat the irradiation and detecting on the first number of pixelsone or more times before irradiating pixels of a second number of pixelsthat are different from the pixels of the first number of pixels in thearray; and (iii) code means for selecting the first number of pixelsbased on information on the adequate period for the fluorescent materialin a pixel to recover from a metastable state.